13-44224061-C-T

Variant names:

• chr13-44224061-C-T
• rs2248414
• ENST00000437867.6:n.1492-14767C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000618753.4(SMIM2-AS1):​n.412-14767C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 152,054 control chromosomes in the GnomAD database, including 7,198 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.30 (7198 hom., cov: 32)
• Consequence: SMIM2-AS1 ENST00000618753.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.490

Genes affected

SMIM2-AS1 (HGNC:42674): (SMIM2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMIM2-AS1	ENST00000437867.6	n.1492-14767C>T		intron_variant	Intron 2 of 2	5
SMIM2-AS1	ENST00000618753.4	n.412-14767C>T		intron_variant	Intron 3 of 3	4
SMIM2-AS1	ENST00000659169.2	n.613-14767C>T		intron_variant	Intron 3 of 3
SMIM2-AS1	ENST00000666499.1	n.707-14767C>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44995 AN: 151936 Hom.: 7190 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.307

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.296 AC: 45024 AN: 152054 Hom.: 7198 Cov.: 32 AF XY: 0.296 AC XY: 21965 AN XY: 74328

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.320

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.361

Gnomad4 OTH AF: 0.305

Alfa AF: 0.344 Hom.: 18931

Bravo AF: 0.290

Asia WGS AF: 0.269 AC: 937 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.0
DANN	Benign	0.44

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2248414; hg19: chr13-44798197;